[gmx-users] pair distribution function
ask.archana at gmail.com
Sun Oct 6 16:46:45 CEST 2013
On Sun, Oct 6, 2013 at 8:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/6/13 10:36 AM, Archana Sonawani-Jagtap wrote:
>> I have simulations for different peptides in POPC bilayer.
>> I want to calculate pair distribution function (pdf) between negatively
>> charged phosphate residue of POPC and positively charged residues of
>> peptide. Is there any tool available in gromacs for plotting these values?
> The closest you can get with a built-in Gromacs program is a radial
> distribution function with g_rdf.
> Secondly, how to calculate the center of mass for a bilayer?
> g_traj -ox -com
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
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